Contacts of the strand formed by residues 3121 - 3131 (chain D) in PDB entry 1W21
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU3121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1114B ILE* 4.4 17.7 - - + -
3119D HIS 4.2 0.4 + - - -
3120D ILE* 1.3 84.4 - - - +
3122D VAL* 1.3 62.9 + - - +
3123D THR* 3.6 15.5 + - + +
3141D SER* 4.0 20.2 - - - +
3144D THR 3.3 24.2 - - - +
3145D THR* 4.0 1.1 - - + +
3146D LEU* 4.4 1.5 - - - +
3165D ILE* 4.0 20.0 - - + -
3173D PRO* 2.8 13.0 + - - +
3174D SER 3.6 22.4 - - - +
3175D PRO* 3.9 25.6 - - + -
3178D THR* 3.7 12.8 - - + +
3448D SER* 4.3 3.3 + - - -
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Residues in contact with VAL3122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3121D LEU* 1.3 71.7 - - - +
3123D THR* 1.3 66.7 + - - +
3141D SER* 3.4 2.6 + - - -
3142D GLN* 2.9 50.3 + - + -
3144D THR* 2.8 20.9 + - + +
3145D THR 3.6 7.2 - - - +
3146D LEU* 3.4 38.1 - - + +
3151D ALA* 4.0 9.9 - - + -
3154D THR* 3.9 8.3 - - - +
3446D TRP* 5.3 0.4 - - + -
3447D THR 3.2 27.1 - - - +
3448D SER* 3.6 6.5 - - - +
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Residues in contact with THR3123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3121D LEU 3.6 12.6 + - - +
3122D VAL* 1.3 82.2 - - - +
3124D ARG* 1.3 73.4 + - - +
3139D ALA* 3.9 16.5 - - + +
3140D LEU 3.3 10.5 - - - -
3141D SER* 4.2 3.4 - - - -
3142D GLN* 4.7 1.8 - - - +
3162D ARG* 4.1 2.7 - - - -
3165D ILE* 4.0 27.1 - - + -
3167D TRP* 5.5 0.3 - - - -
3173D PRO* 4.1 16.0 - - + +
3447D THR 4.0 3.3 - - - +
3448D SER* 3.2 16.8 + - - -
3449D ASN* 2.6 34.9 + - - -
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Residues in contact with ARG3124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3123D THR* 1.3 82.5 - - - +
3125D GLU* 1.3 101.6 + - - +
3126D PRO* 3.3 3.5 - - - -
3139D ALA* 3.9 0.9 - - - +
3140D LEU* 3.0 24.1 + - - +
3142D GLN* 5.4 2.7 - - - +
3157D ASP* 4.4 6.0 + - - -
3162D ARG* 3.8 5.8 - - - +
3378D ARG* 4.0 3.6 - - - +
3412D TYR* 3.3 33.3 - - - -
3433D GLU* 2.7 36.5 + - - +
3435D ILE* 3.7 19.0 - - - +
3447D THR* 3.9 28.0 - - + +
3448D SER 4.4 5.8 - - - +
3449D ASN* 3.1 10.3 - - - +
4477D SIA 2.9 24.7 + - - +
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Residues in contact with GLU3125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3124D ARG* 1.3 110.8 + - - +
3126D PRO* 1.3 66.7 - - - +
3127D TYR* 3.6 14.2 - - - -
3139D ALA* 3.8 5.9 - - - -
3140D LEU* 3.7 22.6 + - + +
3157D ASP* 4.4 2.3 - - - +
3162D ARG* 3.1 26.8 + - - -
3234D GLU* 4.2 18.4 - - + +
3412D TYR* 3.9 27.8 - - + -
3433D GLU* 2.8 14.6 + - - -
4477D SIA 3.1 30.2 + - - +
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Residues in contact with PRO3126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3124D ARG 3.3 2.7 - - - -
3125D GLU* 1.3 97.2 - - - +
3127D TYR* 1.3 68.6 + - - +
3138D PHE 3.1 15.3 - - - +
3139D ALA* 3.7 9.9 - - + -
3234D GLU 3.7 1.0 - - - +
3412D TYR* 5.1 1.4 - - + +
3431D TYR* 3.0 25.4 + - + -
3433D GLU* 3.3 37.7 - - + +
3449D ASN* 3.5 16.8 - - - +
3451D ILE* 3.7 26.2 - - + -
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Residues in contact with TYR3127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3125D GLU 3.6 9.0 - - - -
3126D PRO* 1.3 80.6 - - - +
3128D LEU* 1.4 74.0 + - - +
3129D SER* 4.8 0.9 - - - -
3137D MET* 3.5 3.8 - - - +
3138D PHE* 2.7 63.8 + + + +
3140D LEU* 6.1 0.4 - - + -
3164D LEU* 3.4 15.9 - - + +
3187D SER* 3.0 27.6 + - - -
3188D THR* 3.4 21.2 - - - -
3189D SER* 3.6 11.8 + - - -
3234D GLU* 3.2 24.0 - - - -
3235D SER* 3.5 21.3 - - - -
3236D GLU* 3.7 8.7 - - + -
3431D TYR* 3.4 28.7 - - + +
3451D ILE* 4.9 0.3 - - - +
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Residues in contact with LEU3128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3127D TYR* 1.4 87.9 - - - +
3129D SER* 1.3 65.9 + - - +
3135D CYS* 5.1 0.7 - - + -
3136D ARG 3.3 11.7 - - - +
3137D MET* 3.5 28.5 - - + -
3138D PHE* 4.4 0.4 - - - -
3169D MET* 3.9 26.5 - - + -
3236D GLU* 3.7 8.7 + - - +
3415D ALA 4.9 0.3 - - - +
3416D PHE* 3.3 50.1 - - + +
3431D TYR* 3.6 30.4 - - + -
3451D ILE* 3.9 19.1 - - + -
3453D ALA* 4.1 9.0 - - + -
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Residues in contact with SER3129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3127D TYR* 4.8 2.9 - - - -
3128D LEU* 1.3 77.9 - - - +
3130D CYS* 1.3 65.2 + - - +
3136D ARG* 3.0 30.4 + - - +
3138D PHE* 3.6 14.4 - - - -
3189D SER 3.9 2.2 + - - -
3190D CYS* 4.1 3.1 - - - -
3191D HIS 4.7 0.3 + - - -
3196D ARG* 2.9 37.7 + - - -
3236D GLU* 2.8 30.1 + - - +
3416D PHE* 4.9 0.2 - - - -
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Residues in contact with CYS3130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3129D SER* 1.3 78.6 + - - +
3131D ASP* 1.3 63.0 + - - +
3134D GLY 3.1 7.4 - - - +
3135D CYS* 2.1 45.5 - - - -
3191D HIS* 3.6 3.1 + - - +
3196D ARG* 3.0 15.4 + - - -
3236D GLU* 3.9 4.9 + - - +
3416D PHE* 4.0 19.7 - - - -
3417D ILE 4.0 2.9 + - - +
3418D ASP* 3.8 31.2 - - - +
3420D TRP* 3.2 19.1 - - + -
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Residues in contact with ASP3131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2217C ARG* 2.9 18.2 + - - -
3088D ARG* 4.8 4.6 + - - -
3130D CYS* 1.3 75.5 - - - +
3132D PRO* 1.3 77.4 - - + +
3133D GLN* 2.8 34.3 + - - +
3134D GLY 2.8 19.3 + - - -
3136D ARG* 4.7 14.3 - - - -
3191D HIS* 3.4 24.2 - - + -
3196D ARG* 4.4 7.2 + - - +
3420D TRP* 3.6 13.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il